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Temperature and dissolved oxygen concentration are important abiotic factors that can limit the growth and survival of sea cucumbers by affecting their immune systems. As global warming intensifies, sea cucumbers are increasingly exposed to adverse environmental conditions, which can cause severe economic losses and limit the sustainable development of sea cucumber aquaculture. It is therefore important to better understand how sea cucumbers respond to environmental stress, especially with regard to its effects on immunity. In the present study, the time series of immunity-related gene expression in sea cucumbers under thermal and hypoxic stresses were analyzed separately. The expression trends of 17 genes related to the nuclear factor κB (NF-κB) pathway, the protease family, the complement system, heat shock proteins (HSPs) and the transferrin family during exposure to two stresses at eight time points were concluded. These genes have interconnected roles in stress defense. The expression levels of genes relating to the NF-κB pathways and HSPs were strongly affected in the sea cucumber thermal stress response, while melanotransferrin (Mtf), ferritin (Ft) and mannan-binding C-type lectin (MBCL) were affected by hypoxia. In contrast, complement factor B (Bf), myosin V (Mys) and serine protease inhibitor (SPI) were not that sensitive during the initial period of environmental stress. Similar expression patterns under both thermal and hypoxic stress for certain genes, including an increase in Hsp90 and decreases in lysozyme (Lys), major yolk protein (MYP) and cathepsin C (CTLC) were observed in sea cucumbers. Conversely, NF-κB and Hsp70 were differentially affected by the two stress treatments. Lysozyme-induced immune defense was inconstant in sea cucumbers coping with stress. A gene ontology (GO) analysis of the selected genes revealed that the most co-involved terms related to immunity and iron ion. Our analysis suggests that sea cucumbers demonstrate complex and varied immune responses to different types of stresses. This dynamic image of the immune responses and stress tolerance of sea cucumbers provides new insights into the adaptive strategies of holothurians in adverse environments., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

FOXP3+ regulatory T (Treg) cells are indispensable for immune homeostasis, but their study in humans is complicated by heterogeneity within Treg, the difficulty in purifying Tregs using surface marker expression (e.g. CD25) and the transient expression of FOXP3 by activated effector cells. Here, we report that expression of CD39 and CD45RO distinguishes three sub-populations within human CD4(+)CD25(hi) T cells. Initial phenotypic and functional analysis demonstrated that CD4(+)CD25(hi)CD39(+)CD45RO(+) cells had properties consistent with effector Treg, CD4(+)CD25(hi)CD39(-)CD45RO(-) cells were naïve Treg and CD4(+)CD25(hi)CD39(-)CD45RO(+) cells were predominantly non-Treg with effector T-cell function. Differences in these two newly identified Treg subsets were corroborated by studies of gene expression and TCR analysis. To apply this approach, we studied these two newly identified Treg subsets in ankylosing spondylitis, and showed impairment in both effector and naïve Treg. This work highlights the importance of discriminating Treg subsets to enable proper comparisons of immune regulatory capacity in healthy individuals and those with inflammatory disease.

Interspecific crosses that fuse the genomes of two different species may result in overall gene expression changes in the hybrid progeny, called 'transcriptome shock'. To better understand the expression pattern after genome merging during the early stages of allopolyploid formation, we performed RNA sequencing analysis on developing embryos of Brassica rapa, B. napus, and their synthesized allotriploid hybrids. Here, we show that the transcriptome shock occurs in the developing seeds of the hybrids. Of the homoeologous gene pairs, 17.1% exhibit expression bias, with an overall expression bias toward B. rapa. The expression level dominance also biases toward B. rapa, mainly induced by the expression change in homoeologous genes from B. napus. Functional enrichment analysis revealed significant differences in differentially expressed genes (DEGs) related to photosynthesis, hormone synthesis, and other pathways. Further study showed that significant changes in the expression levels of the key transcription factors (TFs) could regulate the overall interaction network in the developing embryo, which might be an essential cause of phenotype change. In conclusion, the present results have revealed the global changes in gene expression patterns in developing seeds of the hybrid between B. rapa and B. napus, and provided novel insights into the occurrence of transcriptome shock for harnessing heterosis. [ABSTRACT FROM AUTHOR]

Chinese sturgeon (Acipenser sinensis) is a critically endangered fish inhabiting the Yangtze River and Chinese coastal waters. Numerous research projects and conservation efforts have focused on artificial propagation and release to restore this endangered species. However, genomic and full-length transcriptomic sequencing of Chinese sturgeon has rarely been reported. In this study, a total of 10 Chinese sturgeon tissues were used for PacBio Iso-seq and RNA-seq analyses. A total of 19,538 full-length transcripts were obtained with sizes from 51 bp to 7,033 bp. Moreover, cluster analysis of gene families and phylogenetic analysis of 14 species were performed. Furthermore, lncRNAs and coding sequence (CDS) were identified in all Chinese sturgeon tissues. Finally, gene expression profiles and differentially expressed genes (DEGs) were analyzed among 10 tissues in Chinese sturgeon. Taken together, full-length transcripts and the gene expression profile from Chinese sturgeon tissues will provide gene sequences and expression information for future functional genomic study and be very helpful for comprehensive understanding of the genetic mechanism of endangerment in Chinese sturgeon. [ABSTRACT FROM AUTHOR]

Simple Summary: The sea cucumber Apostichopus japonicus is an ecologically significant echinoderm with considerable nutritional and therapeutic value. Color variation of A. japonicus is one of its most important cultivation traits, as color affects its bioactive compounds, taste, and market price. Microphthalmia-associated transcription factor (MITF) is one of the most critical genes in melanocyte development and melanin synthesis pathways. However, how MITF regulates body color and differentiation in sea cucumbers is poorly understood. Here, we analyzed the expression level and location of MITF in white, purple, and green sea cucumbers and identified the genes regulated by MITF using chromatin immunoprecipitation followed by sequencing. Our findings suggested that MITF contributed to the body color differentiation of green, purple, and white sea cucumbers A. japonicus through expression differences and regulation of downstream genes. These findings give researchers a foundation for further research into the processes that underlie the development of body color in sea cucumbers and provide light on how genes are regulated. The results will also provide support for sea cucumber breeding and a useful theoretical basis in order to contribute to the development of the sea cucumber industry. Melanin, which is a pigment produced in melanocytes, is an important contributor to sea cucumber body color. MITF is one of the most critical genes in melanocyte development and melanin synthesis pathways. However, how MITF regulates body color and differentiation in sea cucumbers is poorly understood. In this study, we analyzed the expression level and location of MITF in white, purple, and green sea cucumbers and identified the genes regulated by MITF using chromatin immunoprecipitation followed by sequencing. The mRNA and protein expression levels of MITF were all highest in purple morphs and lowest in white morphs. In situ hybridization indicated that MITF mRNA were mainly expressed in the epidermis. We also identified 984, 732, and 1191 peaks of MITF binding in green, purple, and white sea cucumbers, which were associated with 727, 557, and 887 genes, respectively. Our findings suggested that MITF contributed to the body color differentiation of green, purple, and white sea cucumbers through expression differences and regulation of downstream genes. These results provided a basis for future studies to determine the mechanisms underlying body color formation and provided insights into gene regulation in sea cucumbers. [ABSTRACT FROM AUTHOR]

Raphanobrassica (RrRrCrCr, 2n = 4x = 36), which is generated by distant hybridization between the maternal parent Raphanus sativus (RsRs, 2n = 2x = 18) and the paternal parent Brassica oleracea (C°C°, 2n = 2x = 18), displays intermediate silique phenotypes compared to diploid progenitors. However, the hybrid shares much more similarities in silique phenotypes with those of B. oleracea than those of R. sativus. Strikingly, the silique of Raphanobrassica is obviously split into two parts. To investigate the gene expression patterns behind these phenomena, transcriptome analysis was performed on the upper, middle, and lower sections of pods (RCsiu, RCsim, and RCsil), seeds in the upper and lower sections of siliques (RCseu and RCsel) from Raphanobrassica, whole pods (Rsi and Csi) and all seeds in the siliques (Rse and Cse) from R. sativus and B. oleracea. Transcriptome shock was observed in all five aforementioned tissues of Raphanobrassica. Genome-wide unbalanced biased expression and expression level dominance were also discovered, and both of them were toward B. oleracea in Raphanobrassica, which is consistent with the observed phenotypes. The present results reveal the global gene expression patterns of different sections of siliques of Raphanobrassica, pods, and seeds of B. oleracea and R. sativus, unraveling the tight correlation between global gene expression patterns and phenotypes of the hybrid and its parents. [ABSTRACT FROM AUTHOR]

Cytoplasmic polyadenylation element binding protein 4 (CPEB4) could be an important regulator in variety of cancers. However, the biological function and the underlying molecular mechanism of CPEB4 in non‐small cell lung cancer (NSCLC) remains unknown. In this study, we investigated the metastasis role of CPEB4 in NSCLC cells, we knocked down CPEB4 using siRNA. Transwell migration assay and cell invasion assay on Matrigel were presented, and cell migration was also determined by scratch‐healing assay. ROS generation were determined by fluorescence probe DCFH2‐DA. The protein expression was assessed by ELISA and Western blot analysis. LY294002 were used to inhibit PI3 K/Akt signaling. The data showed that knockdown of CPEB4 inhibited the migration and invasion of NSCLC. Moreover, silencing of CPEB4 reduced Snail and MMP‐3 expression in vitro. We also indicated that CPEB4 knockdown increased the ROS expression. Furthermore, we found that silencing of CPEB4 decreased pAkt expression. Taken all together, our data demonstrated that silencing of CPEB4 induces ROS generation, thus suppressing the Akt expression, which finally prevents NSCLC cells invasion and migration. Therefore, CPEB4 may regard as a target to inhibit NSCLC invasion and metastasis through Akt pathway. [ABSTRACT FROM AUTHOR]

Sea cucumber, Apostichopus japonicus is very sensitive to light changes. It is important to study the influence of light on the molecular response of A. japonicus. In this study, RNA-seq provided a general overview of the gene expression profiles of the body walls of A. japonicus exposed to strong light (“light”), normal light (“control”) and fully dark (“dark”) environment. In the comparisons of “control” vs. “dark”, ”control” vs. “light” and “dark” vs. “light”, 1 161, 113 and 1 705 differentially expressed genes (DEGs) were identified following the criteria of |log2ratio|≥1 and FDR≤0.001, respectively. Gene ontology analysis showed that “cellular process” and “binding” enriched the most DEGs in the category of “biological process” and “molecular function”, while “cell” and “cell part” enriched the most DEGs in the category of “cellular component”. And the DEGs were mapped to 214, 41 and 229 pathways in the Kyoto Encyclopedia of Genes and Genomes database, and 51, 2 and 57 pathways were significantly enriched, respectively. Light-specific DEGs identified in this study will be important targets for further investigation to establish the biochemical mechanisms involved in the adaption of this sea cucumber to changes in the level of environmental light. [ABSTRACT FROM AUTHOR]

Sea cucumber , Apostichopus japonicus is an important species for aquaculture, and its behavior and physiology can change in response to changing salinity conditions. For this reason, it is important to understand the molecular responses of A. japonicus when exposed to ambient changes in salinity. In this study, RNA-Seq provided a general overview of the gene expression profiles in the intestine of A. japonicus exposed to high salinity (SD40), normal salinity (SD30) and low salinity (SD20) environments. Screening for differentially expressed genes (DEGs) using the NOISeq method identified 109, 100, and 89 DEGs based on a fold change of ≥ 2 and divergence probability ≥ 0.8 according to the comparisons of SD20 vs. SD30, SD20 vs.SD40, and SD30 vs. SD40, respectively. Gene ontology analysis showed that the terms “metabolic process” and “catalytic activity” comprised the most enriched DEGs. These fell into the categories of “biological process” and “molecular function”. While “cell” and “cell part” had the most enriched DEGs in the category of “cellular component”. With these DEGs mapping to 2119, 159, and 160 pathways in the Kyoto Encyclopedia of Genes and Genomes database. Of these 51, 2, and 57 pathways were significantly enriched, respectively. The osmosis-specific DEGs identified in this study of A. japonicus will be important targets for further studies to understand the biochemical mechanisms involved with the adaption of sea cucumbers to changes in salinity. [ABSTRACT FROM AUTHOR]

Sea cucumbers are excellent models for studying organ regeneration due to their striking capacity to regenerate most of their viscera after evisceration. In this study, we applied NMR-based metabolomics to determine the metabolite changes that occur during the process of intestine regeneration in sea cucumbers. Partial least-squares discriminant analysis showed that there was significant differences in metabolism between regenerative intestines at 3, 7, and 14 days post evisceration (dpe) and normal intestines. Changes in the concentration of 13 metabolites related to regeneration were observed and analyzed. These metabolites included leucine, isoleucine, valine, arginine, glutamate, hypotaurine, dimethylamine, N , N -dimethylglycine, betaine, taurine, inosine, homarine, and histidine. Three important genes (betaine-aldehyde dehydrogenase, betaine-homocysteine S -methyltransferase 1, and dimethylglycine dehydrogenase) were differentially expressed to regulate the levels of betaine and N , N -dimethylglycine during intestine regeneration. These results provide an important basis for studying regenerative mechanisms and developing regenerative matrixes. [ABSTRACT FROM AUTHOR]

MiRNAs function in post-transcriptional regulation of gene expression and play very important roles in plant development. Lonicera japonica is one of the important medicinal plants in China. However, few studies on the discovery of conserved and novel miRNAs from L. japonica were reported. In this study, we employed deep sequencing technology to identify miRNAs in leaf and flower tissues of L. japonica. A total of 22.97 million clean reads from flower and leaf tissues were obtained, which generated 146 conserved miRNAs distributed in 20 families and 110 novel miRNAs. Accordingly, 72 differentially expressed miRNAs (P≤0.001) between leaves and flowers and their potential target genes were identified and validated. The qRT-PCR validation showed that majority of the differentially expressed miRNAs showed significant tissue-specific expression in L. japonica. Furthermore, the miRNA-mRNA and mRNA-mRNA regulatory networks were constructed using Cytoscape software. Taken together, this study identified a large number of miRNAs and target genes in L. japonica, which not only provides the first global miRNA expression profiles, but also sheds light on functional genomics research on L. japonica in the future. [ABSTRACT FROM AUTHOR]

Abstract: Modulating ion channel function includes acutely affecting the kinetics of the ion channels and chronically changing the expression of ion channels. Our previous study showed that angiotensin II (Ang II) acutely increased hyperpolarization-activated cyclic nucleotide-gated (HCN) currents in nodose ganglion (NG) neurons via NADPH oxidase-superoxide signaling. Therefore, the present study was to measure chronic treatment with Ang II on protein expression of the HCN channels in the primary cultured rat NG neurons. Immunofluorescent staining data showed that HCN1 was expressed in the A-type NG neurons, and HCN2 was expressed in the C-type NG neurons. Chronic treatment of Ang II (100nM, 12h) induced the protein expression of HCN2 besides the overexpression of HCN1 in the A-type NG neurons; and the overexpression of HCN2 in the C-type NG neurons. An Ang II type I receptor antagonist (1μM losartan), a NADPH oxidase inhibitor (100μM apocynin), or a superoxide dismutase mimetic (1mM tempol) attenuated the effect of Ang II to increase the protein expression of the HCN channels in rat nodose neurons. Whole cell patch-clamp data further confirmed that chronic treatment of Ang II (100nM, 12h) significantly enhanced the density of HCN currents in A- and C-type NG neurons. Above three inhibitors significantly inhibited the Ang II-induced increase of the HCN channel density in rat NG neurons. These findings suggest that Ang II-NADPH oxidase-superoxide signaling chronically regulates the protein expression of the HCN channels in rat nodose neurons. [Copyright &y& Elsevier]

CO 2 -induced ocean acidification and warming pose ecological threats to marine life, especially calcifying species such as echinoderms, who rely on biomineralization for skeleton formation. However, previous studies on echinoderm calcification amid climate change had a strong bias towards heavily calcified echinoderms, with little research on lightly calcified ones, such as sea cucumbers. Here, we analyzed the embryo-larval development and their biomineralization–related gene expression of a lightly calcified echinoderm, the sea cucumber (Apostichopus japonicus), under experimental seawater acidification (OA) and/or warming (OW). Results showed that OA (– 0.37 units) delayed development and decreased body size (8.58–56.25 % and 0.36–19.66 % decreases in stage duration and body length, respectively), whereas OW (+3.1 °C) accelerated development and increased body size (33.99–55.28 % increase in stage duration and 2.44–14.41 % enlargement in body length). OW buffered the negative effects of OA on the development timing and body size of A. japonicus. Additionally, no target genes were expressed in the blastula stage, and only two biomineralization genes (colp3α , cyp2) and five TFs (erg , tgif , foxN2/3 , gata1/2/3, and tbr) were expressed throughout the embryo-larval development. Our findings suggest that the low calcification in A. japonicus larvae may be caused by biomineralization genes contraction, and low expression of those genes. Furthermore, this study indicated that seawater acidification and warming affect expression of biomineralization-related genes, and had an effect on body size and development rate during the embryo-larval stage in sea cucumbers. Our study is a first step toward a better understanding of the complexity of high p CO 2 on calcification and helpful for revealing the adaptive strategy of less-calcified echinoderms amid climate change. [Display omitted] • A skeletogenic GRN in early development of holothurians was speculated. • Ocean acidification and warming affect biomineralization-related genes expression. • Acidification delayed development and shortened body length. • Warming mitigated negative effects of acidification. [ABSTRACT FROM AUTHOR]

The carotenoid composition and content in the yellow sarcocarp peach are a direct indicator of quality. Therefore, discoveries regarding the identification of candidate genes related to carotenoid accumulation and their regulatory mechanisms would be beneficial for yellow sarcocarp peach breeding. In this study, the white sarcocarp peach cultivar '21shiji' (21SJ) and its unique yellow sarcocarp bud mutation individual (21BM) were used for carotenoid determination and candidate gene discovery based on UPLC-APCI-MS/MS and RNA-seq. In total, 11 carotenoid compositions showed significant differences between '21SJ' and '21BM', including four carotenes and seven xanthophylls. Furthermore, the accumulation of β-carotene, zeaxanthin, β-cryptoxanthin, antheraxanthin, violaxanthin, and capsanthin showed different tendencies between '21SJ' and '21BM' during the ripening stage and influenced '21BM' yellow sarcocarp formation. Using transcriptome analysis, we found that the differential expression of candidate genes PpZEP , PpVDE1 , PpCCD4 , and PpCCS were major influencing factors. Two transfactors, PpbHLH14 and PpMYB73 , were significantly related to PpZEP , PpVDE1 , PpCCD4 , and PpCCS expression and carotenoid accumulation after weighted gene co-expression network analysis. The identified structural genes and transcription factors in this study will further enrich carotenoid accumulation regulatory mechanism in peach and will provide an important theoretical reference for yellow sarcocarp peach breeding. • White (21SJ) and yellow (21BM) sarcocarp peaches were used for carotenoid analysis. • Genes PpZEP , PpVDE1 , PpCCD4 , and PpCCS may play a role in carotenoid synthesis. • Two potential transcription factors were also discovered, PpbHLH14 and PpMYB73. • Multiple structural genes led to carotenoid accumulation and yellow-peach formation. [ABSTRACT FROM AUTHOR]

Wnt genes encode secreted glycoproteins that act as signaling molecules; these molecules direct cell proliferation, migration, differentiation and survival during animal development, maintenance of homeostasis and regeneration. At present, although the regeneration mechanism in Apostichopus japonicus has been studied, there is a little research on the Wnt signaling pathway in A. japonicus . To understand the potential role of the Wnt signaling pathway in A. japonicus , we cloned and sequenced the WntA gene in A. japonicus . Protein localization analysis showed that WntA protein was ubiquitously expressed in epidermal cells, the muscle and submucosa of the intestinal tissue. After stimulation and evisceration, the dynamic changes in expression of the WntA gene and protein showed that WntA was constitutively expressed during different stages of intestine regeneration in A. japonicus , with higher levels during the early wound healing stage and late lumen formation in the residual and nascent intestinal tissues, indicating its response to intestinal regeneration. Simultaneously, cell proliferation and apoptosis analysis showed that the patterns of cell proliferation were similar to the patterns of WntA protein expression during different intestinal regeneration stages in this organism. Taken together, these results suggested that WntA might participate in intestinal regeneration and may be connected with cell proliferation, apoptosis in different intestinal layers. This research could establish a basis for further examination of WntA functions in A. japonicus and Wnt genes in other echinoderms. [ABSTRACT FROM AUTHOR]

Hsp10 and Hsp60 are important heat shock proteins (HSPs), which might be indispensable in the heat shock response and many other physiological processes. We obtained full-length cDNAs of genes hsp10 and hsp60 and classified their mRNA expression levels under thermal stress in the sea cucumber Apostichopus japonicus. Full-length hsp10 cDNA was 1528bp containing a 5′ untranslated region (UTR) of 83bp, a 3′ UTR of 1133bp and an open reading frame (ORF) of 312bp encoding 103 amino acid residues. Full-length hsp60 cDNA was 2560bp containing a 118-bp 5′ UTR, a 678-bp 3′ UTR and a 1764-bp ORF encoding 586 amino acid residues. The deduced amino acid sequences of Hsp10 and Hsp60 shared the highest identity with sequences of the sea urchin Strongylocentrotus purpuratus, and phylogenetic trees showed that the evolution of Hsp10 and Hsp60 was almost in accord with the evolution of species. Further analysis by real-time PCR showed that the expression of hsp10 and hsp60 mRNA was highly up-regulated at 26°C compared with other three groups (20, 22, 24°C), and their expression in the intestine was in a time-dependent manner at 26°C. The results suggested that hsp10 and hsp60 were involved in the heat-shock response in the sea cucumber A. japonicus. [ABSTRACT FROM AUTHOR]